Have had a smilar experience.
Was trying to change the date of my SYD-DXB-MUC booking in A-Class. Seats available if you bring up the SYD-DXB and DXB-MUC flights separately, bring up SYD-DXB-MUC and they disappear.
Also, if your TA has your PNR on the screen, availability disappears too.
Seems this is not unique to EK. Same thing happened to me with EY.